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imagej-elphel
Commit 3fa095d3 authored by Andrey Filippov's avatar Andrey Filippov
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Saving subset of parameters

parent 2f19b216
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Showing with 336 additions and 170 deletions
src/main/java/Aberration_Calibration.java
View file @ 3fa095d3
......@@ -48,6 +48,8 @@ import java.util.regex.Pattern;
//import FocusingField.FocusingFieldMeasurement;
//import FocusingField.MeasuredSample;
import Jama.Matrix; // Download here: http://math.nist.gov/javanumerics/jama/
......@@ -579,6 +581,7 @@ public static MatchSimulatedPattern.DistortionParameters DISTORTION =new MatchSi
panelRun.setLayout(new GridLayout(1, 0, 5, 5));
addButton("Process Calibration Files",panelRun);
addButton("Save",panelRun);
addButton("Save Selected",panelRun);
addButton("Restore",panelRun,color_restore);
addButton("Restore no autoload",panelRun);
addButton("Restore SFE Latest",panelRun,color_restore);
......@@ -1046,11 +1049,18 @@ if (MORE_BUTTONS) {
String fileName= selectKernelsDirectory(PROCESS_PARAMETERS.kernelsDirectory);
if (fileName!=null) PROCESS_PARAMETERS.kernelsDirectory=fileName;
return;
/* ======================================================================== */
/* ======================================================================== */
} else if (label.equals("Save")) {
saveProperties(null,PROCESS_PARAMETERS.kernelsDirectory,PROCESS_PARAMETERS.useXML, PROPERTIES);
return;
/* ======================================================================== */
} else if (label.equals("Save Selected")) {
Properties selectedProperties=new Properties();
selectedProperties.setProperty("selected", "true");
saveProperties(null,PROCESS_PARAMETERS.kernelsDirectory, PROCESS_PARAMETERS.useXML, selectedProperties);
return;
/* ======================================================================== */
} else if (label.equals("Restore") || label.equals("Restore no autoload")) {
......@@ -13010,6 +13020,7 @@ private double [][] jacobianByJacobian(double [][] jacobian, boolean [] mask) {
} else path+=patterns[0];
if (path==null) return;
setAllProperties(properties);
OutputStream os;
try {
os = new FileOutputStream(path);
......@@ -13050,6 +13061,7 @@ private double [][] jacobianByJacobian(double [][] jacobian, boolean [] mask) {
String directory,
boolean useXML,
Properties properties){
setAllProperties(properties); // NEW. Setting properties from current parameters so missing (in the file) parameters will not cause an error
String [] XMLPatterns= {".conf-xml",".xml"};
String [] confPatterns={".conf"};
String [] patterns=useXML?XMLPatterns:confPatterns;
......@@ -13101,42 +13113,159 @@ private double [][] jacobianByJacobian(double [][] jacobian, boolean [] mask) {
}
/* ======================================================================== */
public void setAllProperties(Properties properties){
properties.setProperty("MASTER_DEBUG_LEVEL", MASTER_DEBUG_LEVEL+"");
properties.setProperty("SHOW_AS_STACKS", SHOW_AS_STACKS+"");// Show debug images as stacks (false - individual)
properties.setProperty("FFT_SIZE", FFT_SIZE+"");
properties.setProperty("MAP_FFT_SIZE", MAP_FFT_SIZE+"");// used to find where grid covers the image
properties.setProperty("GAUSS_WIDTH", GAUSS_WIDTH+""); // 0.4 (0 - use Hamming window)
properties.setProperty("FFT_OVERLAP", FFT_OVERLAP+""); // createPSFMap()
properties.setProperty("PSF_SUBPIXEL", PSF_SUBPIXEL+""); // sub-pixel decimation
properties.setProperty("PSF_SAVE_FILE", PSF_SAVE_FILE+"");// save PSF array to a multi-slice TIFF file
properties.setProperty("THREADS_MAX", THREADS_MAX+""); // 100, testing multi-threading, limit maximal number of threads
properties.setProperty("UPDATE_STATUS", UPDATE_STATUS+""); // update ImageJ status info
SIMUL.setProperties( "SIMUL.", properties);
INTERPOLATE.setProperties( "INTERPOLATE.", properties);
INVERSE.setProperties( "INVERSE.", properties);
PSF_PARS.setProperties( "PSF_PARS.", properties);
OTF_FILTER.setProperties( "OTF_FILTER.", properties);
PATTERN_DETECT.setProperties( "PATTERN_DETECT.", properties);
COMPONENTS.setProperties( "COMPONENTS.", properties);
SHOW_RESULTS.setProperties( "SHOW_RESULTS.", properties);
MULTIFILE_PSF.setProperties( "MULTIFILE_PSF.", properties);
PROCESS_PARAMETERS.setProperties("PROCESS_PARAMETERS.", properties);
DISTORTION.setProperties( "DISTORTION.", properties);
LASER_POINTERS.setProperties("LASER.", properties);
FLATFIELD_PARAMETERS.setProperties("FLATFIELD_PARAMETERS.", properties);
PATTERN_PARAMETERS.setProperties ("PATTERN_PARAMETERS.", properties);
LENS_DISTORTION_PARAMETERS.setProperties("LENS_DISTORTION_PARAMETERS.", properties);
EYESIS_CAMERA_PARAMETERS.setProperties("EYESIS_CAMERA_PARAMETERS.", properties);
LASERS.setProperties("LASERS.", properties);
CAMERAS.setProperties("CAMERAS.", properties);
DISTORTION_PROCESS_CONFIGURATION.setProperties("DISTORTION_PROCESS_CONFIGURATION.", properties);
REFINE_PARAMETERS.setProperties("REFINE_PARAMETERS.", properties);
FOCUS_MEASUREMENT_PARAMETERS.setProperties("FOCUS_MEASUREMENT_PARAMETERS.", properties);
MOTORS.focusingHistory.setProperties("FOCUSING_HISTORY.", properties);
GONIOMETER_PARAMETERS.setProperties("GONIOMETER_PARAMETERS.", properties);
ABERRATIONS_PARAMETERS.setProperties("ABERRATIONS_PARAMETERS.", properties);
if (FOCUSING_FIELD!=null) FOCUSING_FIELD.setProperties("FOCUSING_FIELD.", properties);
boolean select= (properties.getProperty("selected")!=null);
boolean select_MASTER_DEBUG_LEVEL=!select;
boolean select_SHOW_AS_STACKS=!select;
boolean select_FFT_SIZE=!select;
boolean select_MAP_FFT_SIZE=!select;
boolean select_GAUSS_WIDTH=!select;
boolean select_FFT_OVERLAP=!select;
boolean select_PSF_SUBPIXEL=!select;
boolean select_PSF_SAVE_FILE=!select;
boolean select_THREADS_MAX=!select;
boolean select_UPDATE_STATUS=!select;
boolean select_SIMUL=!select;
boolean select_INTERPOLATE=!select;
boolean select_INVERSE=!select;
boolean select_PSF_PARS=!select;
boolean select_OTF_FILTER=!select;
boolean select_PATTERN_DETECT=!select;
boolean select_COMPONENTS=!select;
boolean select_SHOW_RESULTS=!select;
boolean select_MULTIFILE_PSF=!select;
boolean select_PROCESS_PARAMETERS=!select;
boolean select_DISTORTION=!select;
boolean select_LASER_POINTERS=!select;
boolean select_FLATFIELD_PARAMETERS=!select;
boolean select_PATTERN_PARAMETERS=!select;
boolean select_LENS_DISTORTION_PARAMETERS=!select;
boolean select_EYESIS_CAMERA_PARAMETERS=!select;
boolean select_LASERS=!select;
boolean select_CAMERAS=!select;
boolean select_DISTORTION_PROCESS_CONFIGURATION=!select;
boolean select_REFINE_PARAMETERS=!select;
boolean select_FOCUS_MEASUREMENT_PARAMETERS=!select;
boolean select_MOTORS_focusingHistory=!select;
boolean select_GONIOMETER_PARAMETERS=!select;
boolean select_ABERRATIONS_PARAMETERS=!select;
boolean select_FOCUSING_FIELD=!select;
if (select) {
GenericDialog gd = new GenericDialog("Select parameters to save");
gd.addMessage("===== Individual parameters ======");
gd.addCheckbox("MASTER_DEBUG_LEVEL", select_MASTER_DEBUG_LEVEL);
gd.addCheckbox("SHOW_AS_STACKS", select_SHOW_AS_STACKS);
gd.addCheckbox("FFT_SIZE",select_FFT_SIZE);
gd.addCheckbox("MAP_FFT_SIZE",select_MAP_FFT_SIZE);
gd.addCheckbox("GAUSS_WIDTH",select_GAUSS_WIDTH);
gd.addCheckbox("FFT_OVERLAP",select_FFT_OVERLAP);
gd.addCheckbox("PSF_SUBPIXEL",select_PSF_SUBPIXEL);
gd.addCheckbox("PSF_SAVE_FILE",select_PSF_SAVE_FILE);
gd.addCheckbox("THREADS_MAX",select_THREADS_MAX);
gd.addCheckbox("UPDATE_STATUS",select_UPDATE_STATUS);
gd.addMessage("===== Parameter classes ======");
gd.addCheckbox("SIMUL",select_SIMUL);
gd.addCheckbox("INTERPOLATE",select_INTERPOLATE);
gd.addCheckbox("INVERSE",select_INVERSE);
gd.addCheckbox("PSF_PARS",select_PSF_PARS);
gd.addCheckbox("OTF_FILTER",select_OTF_FILTER);
gd.addCheckbox("PATTERN_DETECT",select_PATTERN_DETECT);
gd.addCheckbox("COMPONENTS",select_COMPONENTS);
gd.addCheckbox("SHOW_RESULTS",select_SHOW_RESULTS);
gd.addCheckbox("MULTIFILE_PSF",select_MULTIFILE_PSF);
gd.addCheckbox("PROCESS_PARAMETERS",select_PROCESS_PARAMETERS);
gd.addCheckbox("DISTORTION",select_DISTORTION);
gd.addCheckbox("LASER_POINTERS",select_LASER_POINTERS);
gd.addCheckbox("FLATFIELD_PARAMETERS",select_FLATFIELD_PARAMETERS);
gd.addCheckbox("PATTERN_PARAMETERS",select_PATTERN_PARAMETERS);
gd.addCheckbox("LENS_DISTORTION_PARAMETERS",select_LENS_DISTORTION_PARAMETERS);
gd.addCheckbox("EYESIS_CAMERA_PARAMETERS",select_EYESIS_CAMERA_PARAMETERS);
gd.addCheckbox("LASERS",select_LASERS);
gd.addCheckbox("CAMERAS",select_CAMERAS);
gd.addCheckbox("DISTORTION_PROCESS_CONFIGURATION",select_DISTORTION_PROCESS_CONFIGURATION);
gd.addCheckbox("REFINE_PARAMETERS",select_REFINE_PARAMETERS);
gd.addCheckbox("FOCUS_MEASUREMENT_PARAMETERS",select_FOCUS_MEASUREMENT_PARAMETERS);
gd.addCheckbox("MOTORS_focusingHistory",select_MOTORS_focusingHistory);
gd.addCheckbox("GONIOMETER_PARAMETERS",select_GONIOMETER_PARAMETERS);
gd.addCheckbox("ABERRATIONS_PARAMETERS",select_ABERRATIONS_PARAMETERS);
gd.addCheckbox("FOCUSING_FIELD",select_FOCUSING_FIELD);
WindowTools.addScrollBars(gd);
gd.showDialog();
if (gd.wasCanceled()) return;
select_MASTER_DEBUG_LEVEL=gd.getNextBoolean();
select_SHOW_AS_STACKS=gd.getNextBoolean();
select_FFT_SIZE=gd.getNextBoolean();
select_MAP_FFT_SIZE=gd.getNextBoolean();
select_GAUSS_WIDTH=gd.getNextBoolean();
select_FFT_OVERLAP=gd.getNextBoolean();
select_PSF_SUBPIXEL=gd.getNextBoolean();
select_PSF_SAVE_FILE=gd.getNextBoolean();
select_THREADS_MAX=gd.getNextBoolean();
select_UPDATE_STATUS=gd.getNextBoolean();
select_SIMUL=gd.getNextBoolean();
select_INTERPOLATE=gd.getNextBoolean();
select_INVERSE=gd.getNextBoolean();
select_PSF_PARS=gd.getNextBoolean();
select_OTF_FILTER=gd.getNextBoolean();
select_PATTERN_DETECT=gd.getNextBoolean();
select_COMPONENTS=gd.getNextBoolean();
select_SHOW_RESULTS=gd.getNextBoolean();
select_MULTIFILE_PSF=gd.getNextBoolean();
select_PROCESS_PARAMETERS=gd.getNextBoolean();
select_DISTORTION=gd.getNextBoolean();
select_LASER_POINTERS=gd.getNextBoolean();
select_FLATFIELD_PARAMETERS=gd.getNextBoolean();
select_PATTERN_PARAMETERS=gd.getNextBoolean();
select_LENS_DISTORTION_PARAMETERS=gd.getNextBoolean();
select_EYESIS_CAMERA_PARAMETERS=gd.getNextBoolean();
select_LASERS=gd.getNextBoolean();
select_CAMERAS=gd.getNextBoolean();
select_DISTORTION_PROCESS_CONFIGURATION=gd.getNextBoolean();
select_REFINE_PARAMETERS=gd.getNextBoolean();
select_FOCUS_MEASUREMENT_PARAMETERS=gd.getNextBoolean();
select_MOTORS_focusingHistory=gd.getNextBoolean();
select_GONIOMETER_PARAMETERS=gd.getNextBoolean();
select_ABERRATIONS_PARAMETERS=gd.getNextBoolean();
select_FOCUSING_FIELD=gd.getNextBoolean();
}
if (select_MASTER_DEBUG_LEVEL) properties.setProperty("MASTER_DEBUG_LEVEL", MASTER_DEBUG_LEVEL+"");
if (select_SHOW_AS_STACKS) properties.setProperty("SHOW_AS_STACKS", SHOW_AS_STACKS+"");// Show debug images as stacks (false - individual)
if (select_FFT_SIZE) properties.setProperty("FFT_SIZE", FFT_SIZE+"");
if (select_MAP_FFT_SIZE) properties.setProperty("MAP_FFT_SIZE", MAP_FFT_SIZE+"");// used to find where grid covers the image
if (select_GAUSS_WIDTH) properties.setProperty("GAUSS_WIDTH", GAUSS_WIDTH+""); // 0.4 (0 - use Hamming window)
if (select_FFT_OVERLAP) properties.setProperty("FFT_OVERLAP", FFT_OVERLAP+""); // createPSFMap()
if (select_PSF_SUBPIXEL) properties.setProperty("PSF_SUBPIXEL", PSF_SUBPIXEL+""); // sub-pixel decimation
if (select_PSF_SAVE_FILE) properties.setProperty("PSF_SAVE_FILE", PSF_SAVE_FILE+"");// save PSF array to a multi-slice TIFF file
if (select_THREADS_MAX) properties.setProperty("THREADS_MAX", THREADS_MAX+""); // 100, testing multi-threading, limit maximal number of threads
if (select_UPDATE_STATUS) properties.setProperty("UPDATE_STATUS", UPDATE_STATUS+""); // update ImageJ status info
if (select_SIMUL) SIMUL.setProperties( "SIMUL.", properties);
if (select_INTERPOLATE) INTERPOLATE.setProperties( "INTERPOLATE.", properties);
if (select_INVERSE) INVERSE.setProperties( "INVERSE.", properties);
if (select_PSF_PARS) PSF_PARS.setProperties( "PSF_PARS.", properties);
if (select_OTF_FILTER) OTF_FILTER.setProperties( "OTF_FILTER.", properties);
if (select_PATTERN_DETECT) PATTERN_DETECT.setProperties( "PATTERN_DETECT.", properties);
if (select_COMPONENTS) COMPONENTS.setProperties( "COMPONENTS.", properties);
if (select_SHOW_RESULTS) SHOW_RESULTS.setProperties( "SHOW_RESULTS.", properties);
if (select_MULTIFILE_PSF) MULTIFILE_PSF.setProperties( "MULTIFILE_PSF.", properties);
if (select_PROCESS_PARAMETERS) PROCESS_PARAMETERS.setProperties("PROCESS_PARAMETERS.", properties);
if (select_DISTORTION) DISTORTION.setProperties( "DISTORTION.", properties);
if (select_LASER_POINTERS) LASER_POINTERS.setProperties("LASER.", properties);
if (select_FLATFIELD_PARAMETERS) FLATFIELD_PARAMETERS.setProperties("FLATFIELD_PARAMETERS.", properties);
if (select_PATTERN_PARAMETERS) PATTERN_PARAMETERS.setProperties ("PATTERN_PARAMETERS.", properties);
if (select_LENS_DISTORTION_PARAMETERS) LENS_DISTORTION_PARAMETERS.setProperties("LENS_DISTORTION_PARAMETERS.", properties);
if (select_EYESIS_CAMERA_PARAMETERS) EYESIS_CAMERA_PARAMETERS.setProperties("EYESIS_CAMERA_PARAMETERS.", properties);
if (select_LASERS) LASERS.setProperties("LASERS.", properties);
if (select_CAMERAS) CAMERAS.setProperties("CAMERAS.", properties);
if (select_DISTORTION_PROCESS_CONFIGURATION) DISTORTION_PROCESS_CONFIGURATION.setProperties("DISTORTION_PROCESS_CONFIGURATION.", properties);
if (select_REFINE_PARAMETERS) REFINE_PARAMETERS.setProperties("REFINE_PARAMETERS.", properties);
if (select_FOCUS_MEASUREMENT_PARAMETERS) FOCUS_MEASUREMENT_PARAMETERS.setProperties("FOCUS_MEASUREMENT_PARAMETERS.", properties);
if (select_MOTORS_focusingHistory) MOTORS.focusingHistory.setProperties("FOCUSING_HISTORY.", properties);
if (select_GONIOMETER_PARAMETERS) GONIOMETER_PARAMETERS.setProperties("GONIOMETER_PARAMETERS.", properties);
if (select_ABERRATIONS_PARAMETERS) ABERRATIONS_PARAMETERS.setProperties("ABERRATIONS_PARAMETERS.", properties);
if ((select_FOCUSING_FIELD) && (FOCUSING_FIELD!=null)) FOCUSING_FIELD.setProperties("FOCUSING_FIELD.", properties);
if (select) properties.remove("selected");
}
/* ======================================================================== */
public void getAllProperties(Properties properties){
......
src/main/java/FocusingField.java
View file @ 3fa095d3
......@@ -340,8 +340,20 @@ public class FocusingField {
System.out.println("fieldFitting is not initialized, nothing to save");
return;
}
fieldFitting.setProperties(prefix+"fieldFitting.",properties);
boolean select= (properties.getProperty("selected")!=null);
boolean select_fieldFitting=!select;
boolean select_FOCUSING_FIELD=!select;
if (select) {
GenericDialog gd = new GenericDialog("Select FocusingField parameters to save");
gd.addCheckbox("FieldFitting parameter class", select_fieldFitting);
gd.addCheckbox("FocusingField local parameters", select_FOCUSING_FIELD);
gd.showDialog();
if (gd.wasCanceled()) return;
select_fieldFitting=gd.getNextBoolean();
select_FOCUSING_FIELD=gd.getNextBoolean();
}
if (select_fieldFitting) fieldFitting.setProperties(prefix+"fieldFitting.",properties);
if (select_FOCUSING_FIELD){
properties.setProperty(prefix+"pX0_distortions",pX0_distortions+"");
properties.setProperty(prefix+"pY0_distortions",pY0_distortions+"");
properties.setProperty(prefix+"currentPX0",currentPX0+"");
......@@ -407,8 +419,8 @@ public class FocusingField {
properties.setProperty(prefix+"rslt_mtf50_mode",rslt_mtf50_mode+"");
properties.setProperty(prefix+"rslt_solve",rslt_solve+"");
for (int chn=0; chn<rslt_show_chn.length; chn++) properties.setProperty(prefix+"rslt_show_chn_"+chn,rslt_show_chn[chn]+"");
// always re-calculate here? - only in calibration mode or restore calibration mode? No, only in LMA in calibration mode
// zRanges=calcZRanges(dataWeightsToBoolean());
// always re-calculate here? - only in calibration mode or restore calibration mode? No, only in LMA in calibration mode
// zRanges=calcZRanges(dataWeightsToBoolean());
if (zRanges!=null){
properties.setProperty(prefix+"zRanges_length",zRanges.length+"");
for (int chn=0;chn<zRanges.length;chn++) if (zRanges[chn]!=null) {
......@@ -419,6 +431,7 @@ public class FocusingField {
}
}
}
}
public void getProperties(String prefix,Properties properties){
savedProperties=properties;
......@@ -4574,13 +4587,36 @@ public boolean LevenbergMarquardt(
if (debugLevel>1) System.out.println ("Mechanical properties not yet initialized, will save properties later");
return;
}
properties.setProperty(prefix+"numberOfLocations",numberOfLocations+"");
properties.setProperty(prefix+"centerSelect_X",centerSelect[0]+"");
properties.setProperty(prefix+"centerSelect_Y",centerSelect[1]+"");
mechanicalFocusingModel.setProperties(prefix+"mechanicalFocusingModel.",properties);
boolean select= (properties.getProperty("selected")!=null);
boolean select_mechanicalFocusingModel=!select;
boolean select_curvatureModel=!select;
boolean select_fieldStrategies=!select;
boolean select_FieldFitting=!select;
if (select) {
GenericDialog gd = new GenericDialog("Select FieldFitting parameters to save");
gd.addCheckbox("MechanicalFocusingModel parameter class", select_mechanicalFocusingModel);
gd.addCheckbox("CurvatureModel parameter classes", select_curvatureModel);
gd.addCheckbox("FieldStrategies parameter classes", select_fieldStrategies);
gd.addCheckbox("FieldFitting local parameters", select_FieldFitting);
gd.showDialog();
if (gd.wasCanceled()) return;
select_mechanicalFocusingModel=gd.getNextBoolean();
select_curvatureModel=gd.getNextBoolean();
select_fieldStrategies=gd.getNextBoolean();
select_FieldFitting=gd.getNextBoolean();
}
if (select_mechanicalFocusingModel) mechanicalFocusingModel.setProperties(prefix+"mechanicalFocusingModel.",properties);
if (select_curvatureModel) {
for (int i=0;i<curvatureModel.length;i++){
if (curvatureModel[i]!=null) curvatureModel[i].setProperties(prefix+"curvatureModel_"+i+".",properties);
}
}
if (select_FieldFitting) {
properties.setProperty(prefix+"numberOfLocations",numberOfLocations+"");
properties.setProperty(prefix+"centerSelect_X",centerSelect[0]+"");
properties.setProperty(prefix+"centerSelect_Y",centerSelect[1]+"");
if (channelSelect!=null) for (int i=0;i<channelSelect.length;i++){
properties.setProperty(prefix+"channelSelect_"+i,channelSelect[i]+"");
}
......@@ -4603,7 +4639,7 @@ public boolean LevenbergMarquardt(
properties.setProperty(prefix+"sampleCorrPullZero_"+chn+"_"+i,sampleCorrPullZero[chn][i]+"");
}
// save correction parameters values
// private double [][][] correctionParameters=new double[6][][]; // all
// private double [][][] correctionParameters=new double[6][][]; // all
if (correctionParameters!=null){
for (int chn=0;chn<correctionParameters.length; chn++) if (correctionParameters[chn]!=null){
for (int np=0;np<correctionParameters[chn].length;np++) if (correctionParameters[chn][np]!=null){
......@@ -4613,7 +4649,8 @@ public boolean LevenbergMarquardt(
}
}
}
fieldStrategies.setProperties(prefix+"fieldStrategies.",properties);
}
if (select_fieldStrategies) fieldStrategies.setProperties(prefix+"fieldStrategies.",properties);
}
public void getProperties(String prefix,Properties properties){
if (properties.getProperty(prefix+"numberOfLocations")!=null)
......
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